Search results for the GEO ID: GSE8998 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM228465 | GPL341 |
|
iron biological rep1
|
untreated rat kidney glomeruli
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228465
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Paired kidneys from both normal and anti-Thy1.1 rats were collected. Following a mid-line incision, the aorta was cannulated and one kidney perfused with iron oxide particles (NDT vol 9 p304). The renal artery of the contra-lateral kidney was clamped to prevent its perfusion by iron oxide. Iron oxide containing glomeruli from the perfused kidney were isolated by a combined sieving technique and magnetic purification; this technique resulted in a glomerular purity of >99% by phase contrast microscopy. Total RNA from glomeruli was extracted using Trizol (Invitrogen, Carlsbad, CA) as per the manufacturer's instructions with only minor modifications. The quality of all RNA samples was assured by evaluation on an Agilent Technologies 2100 Bioanalyzer (Palo Alto, CA).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228465/suppl/GSM228465.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228465/suppl/GSM228465.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228466 | GPL341 |
|
iron biological rep2
|
untreated rat kidney glomeruli
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228466
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Paired kidneys from both normal and anti-Thy1.1 rats were collected. Following a mid-line incision, the aorta was cannulated and one kidney perfused with iron oxide particles (NDT vol 9 p304). The renal artery of the contra-lateral kidney was clamped to prevent its perfusion by iron oxide. Iron oxide containing glomeruli from the perfused kidney were isolated by a combined sieving technique and magnetic purification; this technique resulted in a glomerular purity of >99% by phase contrast microscopy. Total RNA from glomeruli was extracted using Trizol (Invitrogen, Carlsbad, CA) as per the manufacturer's instructions with only minor modifications. The quality of all RNA samples was assured by evaluation on an Agilent Technologies 2100 Bioanalyzer (Palo Alto, CA).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228466/suppl/GSM228466.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228466/suppl/GSM228466.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228467 | GPL341 |
|
iron biological rep3
|
untreated rat kidney glomeruli
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228467
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Paired kidneys from both normal and anti-Thy1.1 rats were collected. Following a mid-line incision, the aorta was cannulated and one kidney perfused with iron oxide particles (NDT vol 9 p304). The renal artery of the contra-lateral kidney was clamped to prevent its perfusion by iron oxide. Iron oxide containing glomeruli from the perfused kidney were isolated by a combined sieving technique and magnetic purification; this technique resulted in a glomerular purity of >99% by phase contrast microscopy. Total RNA from glomeruli was extracted using Trizol (Invitrogen, Carlsbad, CA) as per the manufacturer's instructions with only minor modifications. The quality of all RNA samples was assured by evaluation on an Agilent Technologies 2100 Bioanalyzer (Palo Alto, CA).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228467/suppl/GSM228467.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228467/suppl/GSM228467.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228468 | GPL341 |
|
iron biological rep4
|
untreated rat kidney glomeruli
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228468
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Paired kidneys from both normal and anti-Thy1.1 rats were collected. Following a mid-line incision, the aorta was cannulated and one kidney perfused with iron oxide particles (NDT vol 9 p304). The renal artery of the contra-lateral kidney was clamped to prevent its perfusion by iron oxide. Iron oxide containing glomeruli from the perfused kidney were isolated by a combined sieving technique and magnetic purification; this technique resulted in a glomerular purity of >99% by phase contrast microscopy. Total RNA from glomeruli was extracted using Trizol (Invitrogen, Carlsbad, CA) as per the manufacturer's instructions with only minor modifications. The quality of all RNA samples was assured by evaluation on an Agilent Technologies 2100 Bioanalyzer (Palo Alto, CA).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228468/suppl/GSM228468.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228468/suppl/GSM228468.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228469 | GPL341 |
|
LCM 800 biological rep1
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228469
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228469/suppl/GSM228469.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228469/suppl/GSM228469.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228470 | GPL341 |
|
LCM 800 biological rep2
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228470
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228470/suppl/GSM228470.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228470/suppl/GSM228470.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228471 | GPL341 |
|
LCM 800 biological rep3
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228471
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228471/suppl/GSM228471.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228471/suppl/GSM228471.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228472 | GPL341 |
|
LCM 800 biological rep4
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228472
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228472/suppl/GSM228472.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228472/suppl/GSM228472.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228473 | GPL341 |
|
LCM 800 biological rep5
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228473
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228473/suppl/GSM228473.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228473/suppl/GSM228473.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228474 | GPL341 |
|
LCM 20 biological rep1
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228474
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228474/suppl/GSM228474.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228474/suppl/GSM228474.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228475 | GPL341 |
|
LCM 20 biological rep2
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228475
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228475/suppl/GSM228475.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228475/suppl/GSM228475.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228476 | GPL341 |
|
LCM 20 biological rep3
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228476
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228476/suppl/GSM228476.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228476/suppl/GSM228476.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
|
GSM228477 | GPL341 |
|
LCM 20 biological rep4
|
rat kidney untreated, laser capture microdissected glomeruli with 2 rounds of RNA amplication
|
Lewis-hsd rat
Age: 18 weeks
|
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
Sample_geo_accession | GSM228477
| Sample_status | Public on Sep 11 2007
| Sample_submission_date | Sep 10 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | no treatment; kidneys were immediately frozen after dissection
| Sample_growth_protocol_ch1 | regular rat diet
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | LCM of approximately 800 glomerular cross-sections (10 micron thick tissue section) followed by Trizol extraction of total RNA was performed according to the manufacturer's instructions; then followed by two rounds of amplification using the Arcturus HS Riboamp kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | GeneChips were scanned using Affymetrix Genechip Scanner 3000.
| Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| Sample_platform_id | GPL341
| Sample_contact_name | Jian,,Zhou
| Sample_contact_email | jzhou@uchicago.edu
| Sample_contact_phone | 773 834 1166
| Sample_contact_department | functional Genomics Facility
| Sample_contact_institute | University of Chicago
| Sample_contact_address | 5841 S Maryland Ave
| Sample_contact_city | Chicago
| Sample_contact_state | IL
| Sample_contact_zip/postal_code | 60637
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228477/suppl/GSM228477.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM228nnn/GSM228477/suppl/GSM228477.CHP.gz
| Sample_series_id | GSE8998
| Sample_data_row_count | 15923
| |
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